Publications

Physique Statistique et Inférence pour la Biologie

51 RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles
Barbara Bravi, Jérôme Tubiana, Simona Cocco, Rémi Monasson, Thierry Mora, Aleksandra M Walczak
Cell Systems

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52 Single molecule microscopy reveals key physical features of repair foci in living cells
Judith Miné-Hattab, Mathias Heltberg, Marie Villemeur, Chloé Guedj, Thierry Mora, Aleksandra Walczak, Maxime Dahan, Angela Taddei
eLife

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53 Contribution of resident and circulating precursors to tumor-infiltrating CD8 + T cell populations in lung cancer
Paul Gueguen, Christina Metoikidou, Thomas Dupic, Myriam Lawand, Christel Goudot, Sylvain Baulande, Sonia Lameiras, Olivier Lantz, Nicolas Girard, Agathe Seguin-Givelet, Marine Lefevre, Thierry Mora, Aleksandra Walczak, Joshua Waterfall, Sebastian Amigorena
Science Immunology

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54 Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection
Anastasia Minervina, Ekaterina Komech, Aleksei Titov, Meriem Bensouda Koraichi, Elisa Rosati, Ilgar Mamedov, Andre Franke, Grigory Efimov, Dmitriy Chudakov, Thierry Mora, Aleksandra Walczak, Yuri Lebedev, Mikhail Pogorelyy
eLife

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55 Survival probability and size of lineages in antibody affinity maturation
Marco Molari, Rémi Monasson, Simona Cocco
Physical Review E

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56 Parameters and determinants of responses to selection in antibody libraries
Steven Schulz, Sébastien Boyer, Matteo Smerlak, Simona Cocco, Rémi Monasson, Clément Nizak, Olivier Rivoire
PLoS Computational Biology

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57 Online characterization of the retinal network
Baptiste Lefebvre
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58 Population variability in the generation and thymic selection of T-cell repertoires
Zachary Sethna, Giulio Isacchini, Thomas Dupic, Thierry Mora, Aleksandra Walczak, Yuval Elhanati
PLoS Computational Biology

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59 Modélisation et inférence Bayésienne pour la maturation d'affinité des anticorps
Marco Molari
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60 Low-dimensional continuous attractors in recurrent neural networks : from statistical physics to computational neuroscience
Aldo Battista
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61 Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data
Natanael Spisak, Aleksandra Walczak, Thierry Mora
Nucleic Acids Research

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62 SOS: online probability estimation and generation of T-and B-cell receptors
Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
Bioinformatics

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63 A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute
Jonathan Desponds, Massimo Vergassola, Aleksandra Walczak
eLife

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64 Blind deconvolution for spike inference from fluorescence recordings
Jérôme Tubiana, Sébastien Wolf, Thomas Panier, Georges Debregeas
Journal of Neuroscience Methods

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65 An evolution-based model for designing chorismate mutase enzymes
William P Russ, Matteo Figliuzzi, Christian Stocker, Pierre Barrat-Charlaix, Michael Socolich, Peter Kast, Donald Hilvert, Remi Monasson, Simona Cocco, Martin Weigt, Rama Ranganathan
Science

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66 Building General Langevin Models from Discrete Datasets
Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
Physical Review X

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67 Quantitative modeling of the effect of antigen dosage on B-cell affinity distributions in maturating germinal centers
Marco Molari, Klaus Eyer, Jean Baudry, Simona Cocco, Remi Monasson
eLife

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68 Generative models of T-cell receptor sequences
Giulio Isacchini, Zachary Sethna, Yuval Elhanati, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
Physical Review E

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69 Spectrum of multispace Euclidean random matrices
Aldo Battista, Remi Monasson
Physical Review E

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70 Place-cell' emergence and learning of invariant data with restricted Boltzmann machines: breaking and dynamical restoration of continuous symmetries in the weight space
Moshir Harsh, Jérôme Tubiana, Simona Cocco, Rémi Monasson
Journal of Physics A: Mathematical and Theoretical

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71 Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones
Anastasia Minervina, Mikhail Pogorelyy, Ekaterina Komech, Vadim Karnaukhov, Petra Bacher, Elisa Rosati, Andre Franke, Dmitriy Chudakov, Ilgar Mamedov, Yuri Lebedev, Thierry Mora, Aleksandra M Walczak
eLife

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72 Rapport de conjoncture 2019 : CID 51 Modélisation mathématique, informatique et physique pour les sciences du vivant
Franck Picard, Myriam Ferro, Alice Cleynen, Marie Doumic, Xavier Duchemin, Guillaume Fertin, Jonathan Filee, Philippe Juin, Romain Koszul, Rafael Laboissiere, Dominique Lavenier, Thérèse Malliavin, Antonio Monari, Isabelle Nondier, Françoise Peyrin, Pierre Pouget, David Vallenet, Rufin Vanrullen, Stéphane Vezian, Aleksandra Walczak
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73 Capacity-Resolution Trade-Off in the Optimal Learning of Multiple Low-Dimensional Manifolds by Attractor Neural Networks
Aldo Battista, Rémi Monasson
Physical Review Letters

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74 Inference of compressed Potts graphical models
Francesca Rizzato, Alice Coucke, Eleonora de Leonardis, J. P. P. Barton, Jérôme Tubiana, Remi Monasson, Simona Cocco
Physical Review E

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75 From behavior to circuit modeling of light-seeking navigation in zebrafish larvae
Sophia Karpenko, Sebastien Wolf, Julie Lafaye, Guillaume Le Goc, Thomas Panier, Volker Bormuth, R. Candelier, Georges Debrégeas
eLife

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76 Constraints and limitations on decoding positional information: the Bicoid case-study
Huy Tran, Walczak Aleksandra, Nathalie Dostatni

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77 Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies
Christoph Kreer, Henning Gruell, Thierry Mora, Aleksandra Walczak, Florian Klein
Vaccines

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78 Quantitative Immunology for Physicists
Grégoire Altan-Bonnet, Thierry Mora, Aleksandra M. Walczak
Physics Reports

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79 Inferring the immune response from repertoire sequencing
Maximilian Puelma Touzel, Aleksandra M Walczak, Thierry Mora
PLoS Computational Biology

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80 Gaussian closure scheme for evolving genomes: application to double-peak fitness landscape with short-range epistasis
Eugenio Mauri, Simona Cocco, Rémi Monasson
EPL - Europhysics Letters

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81 Dissipation in Non-Steady State Regulatory Circuits
Paulina Szymańska-Rożek, Dario Villamaina, Jacek Miȩkisz, Aleksandra Walczak
Entropy

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82 Can Grid Cell Ensembles Represent Multiple Spaces?
Davide Spalla, Alexis Dubreuil, Sophie Rosay, Remi Monasson, Alessandro Treves
Neural Computation

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83 How many different clonotypes do immune repertoires contain?
Thierry Mora, Aleksandra Walczak
Current Opinion in Systems Biology

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84 Physical Limit to Concentration Sensing in a Changing Environment
Thierry Mora, Ilya Nemenman
Physical Review Letters

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85 Adaptive cluster expansion for Ising spin models
Simona Cocco, Giancarlo Croce, Francesco Zamponi
The European Physical Journal B: Condensed Matter and Complex Systems

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86 OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs
Zachary Sethna, Yuval Elhanati, Curtis G Callan, Aleksandra M. Walczak, Thierry Mora
Bioinformatics

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87 Physique statistique et apprentissage machine : une méthode et trois exemples
Remi Monasson

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88 Size and structure of the sequence space of repeat proteins
Jacopo Marchi, Ezequiel A Galpern, Rocío Espada, Diego U Ferreiro, Aleksandra M. Walczak, Thierry Mora
PLoS Computational Biology

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89 Learning Compositional Representations of Interacting Systems with Restricted Boltzmann Machines: Comparative Study of Lattice Proteins
Jérôme Tubiana, Simona Cocco, Remi Monasson
Neural Computation

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90 How a well-adapting immune system remembers
Andreas Mayer, Vijay Balasubramanian, Aleksandra M. Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America

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91 Receptor crosstalk improves concentration sensing of multiple ligands
Martín Carballo-Pacheco, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, Thierry Mora
Physical Review E

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92 Modeling the Correlated Activity of Neural Populations: A Review
Christophe Gardella, Olivier Marre, Thierry Mora
Neural Computation

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93 Fierce Selection and Interference in B-Cell Repertoire Response to Chronic HIV-1
Armita Nourmohammad, Jakub Otwinowski, Marta Łuksza, Thierry Mora, Aleksandra M Walczak
Molecular Biology and Evolution

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94 Genesis of the αβ T-cell receptor
Thomas Dupic, Quentin Marcou, Aleksandra M. Walczak, Thierry Mora
PLoS Computational Biology

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95 Learning protein constitutive motifs from sequence data
Jérôme Tubiana, Simona Cocco, Remi Monasson
eLife

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96 Multi-Lineage Evolution in Viral Populations Driven by Host Immune Systems
Jacopo Marchi, Michael Lässig, Thierry Mora, Aleksandra M. Walczak
Pathogens

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97 Detecting T cell receptors involved in immune responses from single repertoire snapshots
Mikhail V Pogorelyy, Anastasia Minervina, Mikhail Shugay, Dmitriy Chudakov, Yuri Lebedev, Thierry Mora, Aleksandra M Walczak
PLoS Biology

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98 Epistasis in a Fitness Landscape Defined by Antibody-Antigen Binding Free Energy
Rhys Adams, Justin Kinney, Aleksandra M Walczak, Thierry Mora
Cell Systems

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99 Cost and benefits of clustered regularly interspaced short palindromic repeats spacer acquisition
Serena Bradde, Thierry Mora, Aleksandra M Walczak
Philosophical Transactions of the Royal Society B: Biological Sciences

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